The files in this data release are the raw DNA metagenome sequence files referenced in Chapter 2 of the Bureau of Ocean Energy Management Environmental Studies Program Report entitled "Multidisciplinary Assessment of Deep-Water Coral Ecosystems: Tools to Detect Impacts of Sub-lethal Stress." Chapter 2, written by Christina A. Kellogg, is entitled "Deep-Sea Coral Metagenomes". The CK1-CK12 raw data (.fastq and .csv) files represent a shotgun metagenome dataset from ten unique colonies of the cold-water coral Lophelia pertusa sampled in the western Atlantic Ocean and Gulf of Mexico to examine their microbial metagenomes. The sequences were produced by random shearing of the deoxyribonucleic acid (DNA), construction of a TruSeq library, and sequencing by Argonne National Laboratory on an Illumina HiSeq 2000 sequencing system. The raw data files associated with this study have also been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), under BioProject number PRJNA471489.  For more information, you may contact Christina Kellogg at the USGS St. Petersburg Coastal and Marine Science Center, 600 4th Street South, St. Petersburg, Florida, USA, 33710; Telephone: (727) 502-8128; Email: ckellogg@usgs.gov.

The folder labeled "Lophelia_metagenomes_raw_data_1" contains 6 subdirectories. Subdirectories CK1, CK3, CK4, and CK6 each contain data for one sample. Subdirectories CK2 and CK5 contain data for poorly sequenced samples which were not included in the analysis. The folder labeled "Lophelia_metagenomes_raw_data_2" contains 7 subdirectories. Subdirectories CK7 through CK12 each contain data for one sample. Subdirectory PhiX contains data for a control sequencing run. The data consist of two compressed FASTQ sequence files (paired end sequences for the sample) as well as a .csv file (except for sample CK8, for which no .csv file was provided by the sequencing facility) that contains the flow cell ID number and the 6-base index sequence for that sample. 

Each raw data folder also holds files containing MIMS (minimum information about a metagenome sequence) compliant metadata, based on standards developed by the Genomic Standards Consortium for reporting sequences from metagenomes (Yilmaz and others, 2011, Nature Biotechnology 29:415-420, doi:10.1038/nbt.1823; Field and others, 2008, Nature Biotechnology 26:541-547, doi:10.1038/nbt1360). These files are named "Lophelia_metagenomes_MIMS_compliant_metadata.xlsx" and "Lophelia_metagenomes_MIMS_compliant_metadata.txt".  The column headers in these metadata files are defined as follows:

sample_name: a unique identifier for each sample

sample_title: title of the sample

bioproject_accession: accession number of the BioProject to which the sample belongs; this is a unique accession number under which the raw data files have been submitted to the NCBI Sequence Read Archive

organism: descriptive organism name of the sample; in this case, a metagenome from the coral Lophelia pertusa

collection_date: date of sampling; format is YYYY-MM-DD

env_biome: descriptor of the broad ecological context of a sample

env_feature: descriptor of the local environment

env_material: material that was displaced by the sample prior to the sampling event

geo_loc_name: geographic location name for where the samples were collected

lat_lon: latitude and longitude where the samples were collected; units are decimal
degrees

depth: water depth at which the samples were collected; units are meters

salinity: salinity at which the samples were collected; units are psu (practical salinity units)

samp_collect_device: method or device employed for collecting sample

samp_mat_process: sample material process; describes how the samples were preserved
in the field for later study

source_material_id: identification of the source material from which the sequenced samples
were derived (more specific than host; for example, what part of the host)

temp: water temperature at which coral samples were collected; units are degrees Celsius